Biomod/2011/TeamJapan/Tokyo/Project

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<div id="navigation"> <div id="menu" style="position:static"> <ul> <li><a class="aMain" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo">Home</a></li> <li><a class="aTeam" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Team/Students">Team</a></li> <li><a class="aProject" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Project</a> <!-- <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Overview</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/introduction">Introduction</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Model">Model</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Devices">Devices</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Modes">Modes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> </ul> --> <li><font color="#ffffff">Results</font> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Experiments</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Design</a></li> </ul></li> <!-- <li><a class="Simulation" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a class="DNA design" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Designs</a></li> --> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook">Notes</a></li> <li><a class="aNotebook" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sponsors/">Sponsors</a></li> <li><a class="aSitemap" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sitemap">Sitemap</a></li>

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Project

light

The aim of our project is the construction of an autonomous micrometer-sized molecular robot. We designed and constructed a micrometer-sized molecular robot, “DNA ciliate”, named after water microorganisms, ciliate. The DNA ciliate has three independent functional modes (see the left figure): free moving mode, track walking mode, and light-irradiated gathering mode.

The DNA ciliate consists of a micrometer-sized body and cilia. The micrometer-sized body is made of a microsphere such as a polystyrene microbead, a glass microbead, etc. The cilia are made of deoxyribozymes (single-stranded DNAs with cleaving activity). In the free moving mode, the DNA ciliate move around in a broad space based on the Brownian motion. In addition, the DNA ciliate can walk along a single-stranded DNA track using the deoxyribozyme activity. The DNA ciliate can be gathered up at a UV-irradiated area. The construction of the DNA ciliate is shown in detail below.


The body of the DNA ciliate

DNA ciliates'body
DNA ciliates'body
The DNA ciliate consists of a micrometer-sized body and cilia. The body of the DNA ciliate is made of a polystyrene microbead with a diameter of about 1 μm. The cilia made of deoxyribozymes are attached on the surface of the body with the amide bond (a chemical covalent bond).
Figure.1:The pattern diagram of creating DNA ciliate
Figure.1:The pattern diagram of creating DNA ciliate

Three independent modes of the DNA ciliate

  1. Free moving mode

The DNA ciliate is an autonomously moving molecular robot. The first moving mode is the free moving based on the Brownian motion in an aqueous media. By the free moving mode, the DNA ciliate can move around and explore in a broad range of space. This motion is similar to a random motion of microorganisms when the microorganisms search food.

The principle of free moving

The movement by Brownian motion is described by the right equation (1). The left side of the equation is the mean square displacement of a DNA ciliate. R is the displacement from a default position during the time Δt. The diffusion constant D is described by the right equation (2), where T is a temperature, NA is the Avogadro number, η is a viscosity coefficient, and a is the radius of the DNA ciliate body. The diffusion constant is inversely proportional to the radius of the body. Thus, a DNA ciliate with a smaller body can move more broadly.
The equation of Brownian motion.
The equation of Brownian motion.
The equation of Brownian motion.
The equation of Brownian motion.

2. Track walking mode

The mechanizm of track walking is to move DNA ciliate directionally on the track.
To achive this mode, we needed to come up with the mechanism of walking and the way to make DNA tracks.
We chose the "Deoxyribozyme-substrate reaction" to solve the mechanism of walking. And we also chose the microchannel to solve the problem of making of DNA tracks.
we set three goals to achieve this mode:1.Confirmation of deoxyribozyme activity, 2.Construction of DNA tracks and 3.Confirmation of moving directionally. We show the results of these in the result page.

The mechanism of track walking

This reaction utilizes deoxyribozyme legs and their substrates on the DNA tracks. A deoxyribozyme leg of the DNA ciliate cuts the substrate DNA at an inserted RNA base. Then, the leg dissociates from cut substrate and moves to the near uncut substrate. By repeating this reaction, DNA ciliate can walk along DNA track with substrates.
Figure.1:The mechanism that DNA ciliate moves directionally.
Figure.1:The mechanism that DNA ciliate moves directionally.

Construction of DNA tracks

DNA origami can be appropriately landscape for nanometer-sized moving nanomachines because it can be designed to complex structural DNA tracks. However, as the tracks for our micrometer-sized molecular robot DNA ciliate, DNA origami is not useful because it takes enormous time to make micrometer-sized track from DNA origami that DNA ciliate can move along and we may be not able to complete constructing the tracks by this summer. Therefore, we challenged to make complex structural DNA tracks by using the technology of microfluid mechanics.(The light figure) We show you the principle of making microchannel in the result page. (Link:here)
Figure.2:The schematic diagram of microchannel.
Figure.2:The schematic diagram of microchannel.

  3. Light-irradiated gathering mode

In the light-irradiated gathering mode, DNA ciliates gather at a specific area responding to UV irradiation. This mode is achieved by UV-switching DNA devices.
The UV-switching DNA device has the stem-loop structure which has UV-responsive bases, azobenzenes. Before UV-irradiattion, this DNA device doesn’t trap deoxyribozyme legs of DNA ciliate. After UV irradiation, azobenzenes are isomerized and the DNA device traps deoxyribozyme legs of DNA ciliate. By this reaction, DNA ciliates gather at UV-irradiated area. By using this system, we think movement of DNA ciliates can be controlled.

UV-switching system

Deoxyribozyme, blocking DNA, and UV-switching DNA are used in this system. The UV-switching DNA hybridizes with blocking DNA and deoxyribozyme legs of DNA ciliates don’t hybridize with blocking DNA. This structure is closed state. By UV irradiation, the stem-loop of UV-switching DNA becomes open and branch migration starts, so deoxyribozyme legs of DNA ciliates become trapped by UV-switching-DNA. This structure is open state.
UV-switching DNA has a stem-loop structure which contains two azobenzenes. By spotting UV, azobenzenes are isomerized and this loop becomes open. This opened loop has a complementary part for deoxyribozyme. This UV-switching DNA is complimentary for blocking DNA.